Kantong, a traditional food condiment of the people of Northern Ghana, is produced by fermentation of Ceiba pentandra seeds and cassava flour. Knowledge of the microbiology of the fermentation process will be useful in its technological improvement and starter culture development. There was a drop in the initial pH from 6.9 before fermentation to 4.9 after fermentation with change in color of the product from grayish to dark brown as well as the development of a more desirable flavor. Lactic acid bacteria (LAB) with counts between 106 and 109 cfu/g were isolated on MRS agar and subjected to Gram, catalase and oxidase tests. The LAB were further identified by biochemical and genotypic methods using rep-PCR, (GTG)5 primer, 16S rRNA gene sequencing and carbohydrate assimilation profiling. A total of 331 Lactic acid bacteria were isolated of which 47% were Lactobacillus plantarum , 18% Lactobacillus fermentum, 8% Leuconostoc mesenteroides, 12% Pediococcus acidilactici and 15% as Lactobacillus brevis